
Mathias Weller. LinearTime Tree Containment in Phylogenetic Networks. In RECOMBCG18, Springer, 2018. Keywords: explicit network, from network, from rooted trees, nearlystable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulationvisible network, tree containment. Note: https://arxiv.org/abs/1702.06364.



Hussein A. Hejase,
Natalie VandePol,
Gregory A. Bonito and
Kevin J. Liu. Fast and accurate statistical inference of phylogenetic networks using largescale genomic sequence data. In RECOMBCG18, Springer, 2018. Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction. Note: http://biorxiv.org/content/early/2017/05/01/132795, to appear.



Andreas Gunawan. Solving the Tree Containment Problem for Reticulationvisible Networks in Linear Time. In AlCoB18, Vol. 10849:2436 of LNCS, Springer, 2018. Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulationvisible network, tree containment. Note: https://arxiv.org/abs/1702.04088.



Sebastien Roch and
KunChieh Wang. Circular Networks from Distorted Metrics. In RECOMB18, Vol. 10812:167176 of LNCS, Springer, 2018. Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network. Note: https://arxiv.org/abs/1707.05722.





Guillaume Scholz. New algorithms and mathematical tools for phylogenetics beyond trees. PhD thesis, University of East Anglia, 2018. Keywords: circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness. Note: https://ueaeprints.uea.ac.uk/id/eprint/66952.





Andreas Gunawan,
Bhaskar DasGupta and
Louxin Zhang. A decomposition theorem and two algorithms for reticulationvisible networks. In Information and Computation, Vol. 252:161175, 2017. Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulationvisible network, tree containment. Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.



Bingxin Lu,
Louxin Zhang and
Hon Wai Leong. A program to compute the soft RobinsonFoulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017. Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program iceluPhyloNetwork. Note: http://dx.doi.org/10.1186/s1286401735005.



Jesper Jansson,
Ramesh Rajaby and
WingKin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115126 of LNCS, Springer, 2017. Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance. Note: .



Han Lai,
Maureen Stolzer and
Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMBCG17, Vol. 10562:298320 of LNCS, Springer, 2017. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.





KuangYu Chang,
Yun Cui,
SiuMing Yiu and
WingKai Hon. Reconstructing OneArticulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:3445 of LNCS, Springer, 2017. Keywords: explicit network, from distances, kreticulated, phylogenetic network, phylogeny, reconstruction. Note: https://link.springer.com/content/pdf/10.1007%2F9783319595757.pdf#page=100.



Andreas Gunawan,
Bhaskar DasGupta and
Louxin Zhang. Locating a Tree in a ReticulationVisible Network in Cubic Time. In RECOMB2016, Vol. 9649:266 of LNBI, Springer, 2016. Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulationvisible network, tree containment. Note: http://arxiv.org/abs/1507.02119.



Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197208 of LNCS, springer, 2016. Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://halupecupem.archivesouvertes.fr/hal01226035 .











Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96107 of LNCS, Springer, 2015. Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearlystable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://hal.archivesouvertes.fr/hal01116231/en.





Quan Nguyen and
Teemu Roos. Likelihoodbased inference of phylogenetic networks from sequence data by PhyloDAG. In ALCOB15, Vol. 9199:126140 of LNCS, springer, 2015. Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software. Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.





Misagh Kordi and
Mukul S. Bansal. On the Complexity of DuplicationTransferLoss Reconciliation with NonBinary Gene Trees. In ISBRA15, Vol. 9096:187198 of LNCS, springer, 2015. Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf.



Yun Yu and
Luay Nakhleh. A DistanceBased Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378389 of LNCS, springer, 2015. Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction. Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhlehISBRA15.pdf.





Yun Yu and
Luay Nakhleh. A maximum pseudolikelihood approach for phylogenetic networks. In RECOMBCG15, Vol. 16(Suppl 10)(S10):110 of BMC Genomics, BioMed Central, 2015. Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance. Note: http://dx.doi.org/10.1186/1471216416S10S10.





Leo van Iersel,
Steven Kelk,
Nela Lekic and
Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):4966, 2014. Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1210.3211.
Toggle abstract
"Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest (maf) problem asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic Agreement Forest (maaf) problem has the additional restriction that the components of the forest cannot have conflicting ancestral relations in the input trees. There has been considerable interest in the special cases of these problems in which the input trees are required to be binary. However, in practice, phylogenetic trees are rarely binary, due to uncertainty about the precise order of speciation events. Here, we show that the general, nonbinary version of maf has a polynomialtime 4approximation and a fixedparameter tractable (exact) algorithm that runs in O(4opoly(n)) time, where n = X and k is the number of components of the agreement forest minus one. Moreover, we show that a capproximation algorithm for nonbinary maf and a dapproximation algorithm for the classical problem Directed Feedback Vertex Set (dfvs) can be combined to yield a d(c+3)approximation for nonbinary maaf. The algorithms for maf have been implemented and made publicly available. © 2014 Society for Industrial and Applied Mathematics."



Leo van Iersel and
Steven Kelk. Kernelizations for the hybridization number problem on multiple nonbinary trees. In WG14, Vol. 8747:299311 of LNCS, springer, 2014. Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction. Note: http://arxiv.org/abs/1311.4045.



Jesper Jansson and
Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:6678, 2014. Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.
Toggle abstract
"We consider a generalization of the rooted triplet distance between two phylogenetic trees to two phylogenetic networks. We show that if each of the two given phylogenetic networks is a socalled galled tree with n leaves then the rooted triplet distance can be computed in o(n2.687) time. Our upper bound is obtained by reducing the problem of computing the rooted triplet distance between two galled trees to that of counting monochromatic and almostmonochromatic triangles in an undirected, edgecolored graph. To count different types of colored triangles in a graph efficiently, we extend an existing technique based on matrix multiplication and obtain several new algorithmic results that may be of independent interest: (i) the number of triangles in a connected, undirected, uncolored graph with m edges can be computed in o(m1.408) time; (ii) if G is a connected, undirected, edgecolored graph with n vertices and C is a subset of the set of edge colors then the number of monochromatic triangles of G with colors in C can be computed in o(n2.687) time; and (iii) if G is a connected, undirected, edgecolored graph with n vertices and R is a binary relation on the colors that is computable in O(1) time then the number of Rchromatic triangles in G can be computed in o(n2.687) time. © 2013 Elsevier B.V. All rights reserved."



Ran LibeskindHadas,
YiChieh Wu,
Mukul S. Bansal and
Manolis Kellis. Paretooptimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87i95 of BIO, 2014. Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btu289.
Toggle abstract
"Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Paretooptimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. © 2014 The Author. Published by Oxford University Press. All rights reserved."





Chris Whidden,
Robert G. Beiko and
Norbert Zeh. FixedParameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):14311466, 2013. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance. Note: http://arxiv.org/abs/1108.2664, slides.
Toggle abstract
"We present new and improved fixedparameter algorithms for computing maximum agreement forests of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree pruneandregraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depthbounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems. © 2013 Society for Industrial and Applied Mathematics."



Yufeng Wu. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In RECOMB13, Vol. 7821:291303 of LNCS, springer, 2013. Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction. Note: http://www.engr.uconn.edu/~ywu/Papers/ExactNetRecomb2013.pdf.
Toggle abstract
"Phylogenetic network is a model for reticulate evolution. Hybridization network is one type of phylogenetic network for a set of discordant gene trees, and "displays" each gene tree. A central computational problem on hybridization networks is: given a set of gene trees, reconstruct the minimum (i.e. most parsimonious) hybridization network that displays each given gene tree. This problem is known to be NPhard, and existing approaches for this problem are either heuristics or make simplifying assumptions (e.g. work with only two input trees or assume some topological properties). In this paper, we develop an exact algorithm (called PIRNC ) for inferring the minimum hybridization networks from multiple gene trees. The PIRNC algorithm does not rely on structural assumptions. To the best of our knowledge, PIRN C is the first exact algorithm for this formulation. When the number of reticulation events is relatively small (say four or fewer), PIRNC runs reasonably efficient even for moderately large datasets. For building more complex networks, we also develop a heuristic version of PIRNC called PIRNCH. Simulation shows that PIRNCH usually produces networks with fewer reticulation events than those by an existing method. © 2013 SpringerVerlag."



Mukul S. Bansal,
Eric J. Alm and
Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In RECOMB13, Vol. 7821:113 of LNCS, springer, 2013. Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, polynomial, Program RANGERDTL, reconstruction. Note: http://people.csail.mit.edu/mukul/Bansal_RECOMB2013.pdf.
Toggle abstract
"Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While DuplicationLoss (DL) reconciliation leads to a unique maximumparsimony solution, DuplicationTransferLoss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult the infer the true evolutionary history of the gene family. Here, we present an effective, efficient, and scalable method for dealing with this fundamental problem in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn 2) time, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mapping and event assignments, and to investigate the impact of varying event costs. © 2013 SpringerVerlag."



Hoa Vu,
Francis Chin,
WingKai Hon,
Henry Leung,
Kunihiko Sadakane,
WingKin Sung and
SiuMing Yiu. Reconstructing kReticulated Phylogenetic Network from a Set of Gene Trees. In ISBRA13, Vol. 7875:112124 of LNCS, springer, 2013. Keywords: from rooted trees, kreticulated, phylogenetic network, phylogeny, polynomial, Program ARTNET, Program CMPT, reconstruction. Note: http://grid.cs.gsu.edu/~xguo9/publications/2013_Cloud%20computing%20for%20de%20novo%20metagenomic%20sequence%20assembly.pdf#page=123.
Toggle abstract
"The time complexity of existing algorithms for reconstructing a levelx phylogenetic network increases exponentially in x. In this paper, we propose a new classification of phylogenetic networks called kreticulated network. A kreticulated network can model all levelk networks and some levelx networks with x > k. We design algorithms for reconstructing kreticulated network (k = 1 or 2) with minimum number of hybrid nodes from a set of m binary trees, each with n leaves in O(mn 2) time. The implication is that some levelx networks with x > k can now be reconstructed in a faster way. We implemented our algorithm (ARTNET) and compared it with CMPT. We show that ARTNET outperforms CMPT in terms of running time and accuracy. We also consider the case when there does not exist a 2reticulated network for the input trees. We present an algorithm computing a maximum subset of the species set so that a new set of subtrees can be combined into a 2reticulated network. © 2013 SpringerVerlag."





Alberto Apostolico,
Matteo Comin,
Andreas W. M. Dress and
Laxmi Parida. Ultrametric networks: a new tool for phylogenetic analysis. In Algorithms for Molecular Biology, Vol. 8(7):110, 2013. Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program Ultranet. Note: http://dx.doi.org/10.1186/1748718887.
Toggle abstract
"Background: The large majority of optimization problems related to the inference of distancebased trees used in phylogenetic analysis and classification is known to be intractable. One noted exception is found within the realm of ultrametric distances. The introduction of ultrametric trees in phylogeny was inspired by a model of evolution driven by the postulate of a molecular clock, now dismissed, whereby phylogeny could be represented by a weighted tree in which the sum of the weights of the edges separating any given leaf from the root is the same for all leaves. Both, molecular clocks and rooted ultrametric trees, fell out of fashion as credible representations of evolutionary change. At the same time, ultrametric dendrograms have shown good potential for purposes of classification in so far as they have proven to provide good approximations for additive trees. Most of these approximations are still intractable, but the problem of finding the nearest ultrametric distance matrix to a given distance matrix with respect to the L∞ distance has been long known to be solvable in polynomial time, the solution being incarnated in any minimum spanning tree for the weighted graph subtending to the matrix.Results: This paper expands this subdominant ultrametric perspective by studying ultrametric networks, consisting of the collection of all edges involved in some minimum spanning tree. It is shown that, for a graph with n vertices, the construction of such a network can be carried out by a simple algorithm in optimal time O(n2) which is faster by a factor of n than the direct adaptation of the classical O(n3) paradigm by Warshall for computing the transitive closure of a graph. This algorithm, called UltraNet, will be shown to be easily adapted to compute relaxed networks and to support the introduction of artificial points to reduce the maximum distance between vertices in a pair. Finally, a few experiments will be discussed to demonstrate the applicability of subdominant ultrametric networks.Availability: http://www.dei.unipd.it/~ciompin/main/Ultranet/Ultranet.html. © 2013 Apostolico et al.; licensee BioMed Central Ltd."









Andreas Spillner and
Vincent Moulton. Optimal algorithms for computing edge weights in planar splitnetworks. In Journal of Applied Mathematics and Computing, Vol. 39(12):113, 2012. Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network. Note: http://dx.doi.org/10.1007/s121900110506z.
Toggle abstract
"In phylogenetics, biologists commonly compute split networks when trying to better understand evolutionary data. These graphtheoretical structures represent collections of weighted bipartitions or splits of a finite set, and provide a means to display conflicting evolutionary signals. The weights associated to the splits are used to scale the edges in the network and are often computed using some distance matrix associated with the data. In this paper we present optimal polynomial time algorithms for three basic problems that arise in this context when computing split weights for planar splitnetworks. These generalize algorithms that have been developed for special classes of split networks (namely, trees and outerlabeled planar networks). As part of our analysis, we also derive a Crofton formula for full flat split systems, structures that naturally arise when constructing planar splitnetworks. © 2011 Korean Society for Computational and Applied Mathematics."



ZhiZhong Chen and
Lusheng Wang. Algorithms for Reticulate Networks of Multiple Phylogenetic Trees. In TCBB, Vol. 9(2):372384, 2012. Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CMPT, Program MaafB, reconstruction, software. Note: http://rnc.r.dendai.ac.jp/~chen/papers/rMaaf.pdf.
Toggle abstract
"A reticulate network N of multiple phylogenetic trees may have nodes with two or more parents (called reticulation nodes). There are two ways to define the reticulation number of N. One way is to define it as the number of reticulation nodes in N in this case, a reticulate network with the smallest reticulation number is called an optimal typeI reticulate network of the trees. The better way is to define it as the total number of parents of reticulation nodes in N minus the number of reticulation nodes in N ; in this case, a reticulate network with the smallest reticulation number is called an optimal typeII reticulate network of the trees. In this paper, we first present a fast fixedparameter algorithm for constructing one or all optimal typeI reticulate networks of multiple phylogenetic trees. We then use the algorithm together with other ideas to obtain an algorithm for estimating a lower bound on the reticulation number of an optimal typeII reticulate network of the input trees. To our knowledge, these are the first fixedparameter algorithms for the problems. We have implemented the algorithms in ANSI C, obtaining programs CMPT and MaafB. Our experimental data show that CMPT can construct optimal typeI reticulate networks rapidly and MaafB can compute better lower bounds for optimal typeII reticulate networks within shorter time than the previously best program PIRN designed by Wu. © 2006 IEEE."



Benjamin Albrecht,
Celine Scornavacca,
Alberto Cenci and
Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191197, 2012. Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btr618.
Toggle abstract
"Motivation: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events. Results: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a userfriendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera. Availability and implementation: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems. © The Author 2011. Published by Oxford University Press. All rights reserved."



Hyun Jung Park and
Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213224 of LNCS, springer, 2012. Keywords: explicit network, from unrooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, software. Note: https://www.researchgate.net/profile/Hyun_Jung_Park2/publication/262318595_MURPAR_A_Fast_Heuristic_for_Inferring_Parsimonious_Phylogenetic_Networks_from_Multiple_Gene_Trees/links/54b7e7b50cf269d8cbf58cc4.pdf.
Toggle abstract
"Phylogenetic networks provide a graphical representation of evolutionary histories that involve nontreelike evolutionary events, such as horizontal gene transfer (HGT). One approach for inferring phylogenetic networks is based on reconciling gene trees, assuming all incongruence among the gene trees is due to HGT. Several mathematical results and algorithms, both exact and heuristic, have been introduced to construct and analyze phylogenetic networks. Here, we address the computational problem of inferring phylogenetic networks with minimum reticulations from a collection of gene trees. As this problem is known to be NPhard even for a pair of gene trees, the problem at hand is very hard. In this paper, we present an efficient heuristic, MURPAR, for inferring a phylogenetic network from a collection of gene trees by using pairwise reconciliations of trees in the collection. Given the development of efficient and accurate methods for pairwise gene tree reconciliations, MURPAR inherits this efficiency and accuracy. Further, the method includes a formulation for combining pairwise reconciliations that is naturally amenable to an efficient integer linear programming (ILP) solution. We show that MURPAR produces more accurate results than other methods and is at least as fast, when run on synthetic and biological data. We believe that our method is especially important for rapidly obtaining estimates of genomescale evolutionary histories that can be further refined by more detailed and computeintensive methods. © 2012 SpringerVerlag."



Pawel Górecki and
Jerzy Tiuryn. Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model. In Logic and Program Semantics, Vol. 7230:83105 of LNCS, springer, 2012. Keywords: duplication, explicit network, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1007/9783642294853_7.
Toggle abstract
"An Htree is a formal model of evolutionary scenario. It can be used to represent any processes with gene duplication and loss, horizontal gene transfer (HGT) and speciation events. The model of Htrees, introduced in [26], is an extension of the duplicationloss model (DLmodel). Similarly to its ancestor, it has a number of interesting mathematical and biological properties. It is, however, more computationally complex than the DLmodel. In this paper, we primarily address the problem of inferring Htrees that are compatible with a given gene tree and a given phylogeny of species with HGTs. These results create a mathematical and computational foundation for a more general and practical problem of inferring HGTs from given gene and species trees with HGTs. We also demonstrate how our model can be used to support HGT hypotheses based on empirical data sets. © 2012 SpringerVerlag Berlin Heidelberg."



AnChiang Chu,
Jesper Jansson,
Richard Lemence,
Alban Mancheron and
KunMao Chao. Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. In TAMC12, Vol. 7287:177188 of LNCS, springer, 2012. Keywords: from triplets, galled network, level k phylogenetic network, phylogenetic network. Note: preliminary version.
Toggle abstract
"We study the asymptotic behavior of a new type of maximization recurrence, defined as follows. Let k be a positive integer and p k(x) a polynomial of degree k satisfying p k(0) = 0. Define A 0 = 0 and for n ≥ 1, let A n = max 0≤i<n{A i+n kp k(i/n)}. We prove that lim n→∞A n/n n = sup{pk(x)/1x k : 0≤x<1}. We also consider two closely related maximization recurrences S n and S′ n, defined as S 0 = S′ 0 = 0, and for n ≥ 1, S n = max 0≤i<n{S i + i(ni)(ni1)/2} and S′ n = max 0≤i<n{S′ i + ( 3 ni) + 2i( 2 ni) + (ni)( 2 i)}. We prove that lim n→∞ S′n/3( 3 n) = 2(√31)/3 ≈ 0.488033..., resolving an open problem from Bioinformatics about rooted triplets consistency in phylogenetic networks. © 2012 SpringerVerlag."





Jesper Jansson and
Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In CPM12, Vol. 7354:385398 of LNCS, springer, 2012. Keywords: distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance. Note: http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf.
Toggle abstract
"We consider a generalization of the rooted triplet distance between two phylogenetic trees to two phylogenetic networks. We show that if each of the two given phylogenetic networks is a socalled galled tree with n leaves then the rooted triplet distance can be computed in o(n 2.688) time. Our upper bound is obtained by reducing the problem of computing the rooted triplet distance to that of counting monochromatic and almost monochromatic triangles in an undirected, edgecolored graph. To count different types of colored triangles in a graph efficiently, we extend an existing technique based on matrix multiplication and obtain several new related results that may be of independent interest. © 2012 SpringerVerlag."



Hyun Jung Park and
Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood:
The performance of information criteria. In RECOMBCG'12, Vol. 13(suppl 19):S12 of BMCB, 2012. Keywords: AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://www.biomedcentral.com/14712105/13/S19/S12.



Maureen Stolzer,
Han Lai,
Minli Xu,
Deepa Sathaye,
Benjamin Vernot and
Dannie Durand. Inferring Duplications, Losses, Transfers, and Incomplete Lineage Sorting with NonBinary Species Trees. In ECCB12, Vol. 28(18):i409i415 of BIO, 2012. Keywords: duplication, explicit network, from rooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/bts386.
Toggle abstract
"Motivation: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions.The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. Results: We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile nonbinary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixedparameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. © The Author(s) 2012. Published by Oxford University Press."



ThiHau Nguyen,
JeanPhilippe Doyon,
Stéphanie Pointet,
AnneMuriel Chifolleau Arigon,
Vincent Ranwez and
Vincent Berry. Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. In WABI12, Vol. 7534:123134 of LNCS, springer, 2012. Keywords: duplication, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, reconstruction. Note: http://hal.archivesouvertes.fr/hal00718347/en/.
Toggle abstract
"We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dynamic programming matrix used to compute reconciliations, which allows to speedup the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experimental results on simulated and real data confirm that running times are greatly reduced when considering the abovementioned optimization in comparison to the naïve rearrangement procedure. Results also show that gene trees modified by such NNI rearrangements are closer to the correct (simulated) trees and lead to more correct event predictions on average. The program is available at http://www.atgcmontpellier.fr/ Mowgli/. © 2012 SpringerVerlag."





Adrià Alcalà Mena. Trivalent Graph isomorphism in polynomial time. Master's thesis, Universidad de Cantabria, Spain, 2012. Keywords: distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE. Note: http://arxiv.org/abs/1209.1040.



Katharina Huber,
Vincent Moulton,
Andreas Spillner,
Sabine Storandt and
Radoslaw Suchecki. Computing a consensus of multilabeled trees. In ALENEX12, Pages 8492, 2012. Keywords: duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny. Note: http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf.
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In this paper we consider two challenging problems that arise in the context of computing a consensus of a collection of multilabeled trees, namely (1) selecting a compatible collection of clusters on a multiset from an ordered list of such clusters and (2) optimally refining high degree vertices in a multilabeled tree. Forming such a consensus is part of an approach to reconstruct the evolutionary history of a set of species for which events such as genome duplication and hybridization have occurred in the past. We present exact algorithms for solving (1) and (2) that have an exponential runtime in the worst case. To give some impression of their performance in practice, we apply them to simulated input and to a real biological data set highlighting the impact of several structural properties of the input on the performance.



Cayla McBee. Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks. In ISPAN'12, Pages 149155, 2012. Keywords: abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model.
Toggle abstract
"Biologists have been interested in Phylogenetics, the study of evolutionary relatedness among various groups of organisms, for more than 140 years. In spite of this, it has only been in the last 40 years that advances in technology and the availability of DNA sequences have led to statistical, computational and algorithmic work on determining evolutionary relatedness between organisms. One method of determining historical relationships between organisms is to assume a group based evolutionary model and use a discrete Fourier transform. The 1993 paper 'Fourier Calculus on Evolutionary Trees' by L.A. Szekely, M.A. Steel and P.L. Erdos outlines this process. The transform presented in Szekely et al provides an invertible relationship between phylogenetic trees and expected frequencies of nucleotide patterns in nucleotide sequences. This implies that given a set of nucleotide sequences from various organisms it is possible to construct a phylogenetic tree that represents the historical relationships of those organisms. Some scenarios are poorly described by phylogenetic trees and there are biological and statistical reasons for using networks to model phylogenetic relationships. Given this motivation I have generalized Szekely et al's result to apply to a specific type of phylogenetic network known as a splits network. © 2012 IEEE."



Fenglou Mao,
David Williams,
Olga Zhaxybayeva,
Maria S. Poptsova,
Pascal Lapierre,
J. Peter Gogarten and
Ying Xu. Quartet decomposition server: a platform for analyzing phylogenetic trees. In BMCB, Vol. 13:123, 2012. Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program Quartet Decomposition, reconstruction, software, split network.
Toggle abstract
"Background: The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially in phylogenomic analyses. Decomposition of gene trees into embedded quartets (unrooted trees each with four taxa) is a convenient and statistically powerful technique to address this challenging problem. This approach was shown to be useful in several studies of completely sequenced microbial genomes.Results: We present here a web server that takes a collection of gene phylogenies, decomposes them into quartets, generates a Quartet Spectrum, and draws a split network. Users are also provided with various data download options for further analyses. Each gene phylogeny is to be represented by an assessment of phylogenetic information content, such as sets of trees reconstructed from bootstrap replicates or sampled from a posterior distribution. The Quartet Decomposition server is accessible at http://quartets.uga.edu.Conclusions: The Quartet Decomposition server presented here provides a convenient means to perform Quartet Decomposition analyses and will empower users to find statistically supported phylogenetic conflicts. © 2012 Mao et al.; licensee BioMed Central Ltd."



Shlomo Moran,
Sagi Snir and
WingKin Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds. In ACM Transactions on Algorithms, Vol. 7(4), 2011. Keywords: evaluation, galled tree, phylogenetic network. Note: http://www.cs.technion.ac.il/~moran/r/PS/gnetsTOA7Feb2007.pdf.
Toggle abstract
"A coloring of a graph is convex if the vertices that pertain to any color induce a connected subgraph; a partial coloring (which assigns colors to a subset of the vertices) is convex if it can be completed to a convex (total) coloring. Convex coloring has applications in fields such as phylogenetics, communication or transportation networks, etc. When a coloring of a graph is not convex, a natural question is how far it is from a convex one. This problem is denoted as convex recoloring (CR).While the initial works on CR defined and studied the problem on trees, recent efforts aim at either generalizing the underlying graphs or specializing the input colorings. In this work, we extend the underlying graph and the input coloring to partially colored galled networks. We show that although determining whether a coloring is convex on an arbitrary network is hard, it can be found efficiently on galled networks. We present a fixed parameter tractable algorithm that finds the recoloring distance of such a network whose running time is quadratic in the network size and exponential in that distance. This complexity is achieved by amortized analysis that uses a novel technique for contracting colored graphs that seems to be of independent interest. © 2011 ACM."





Celine Scornavacca,
Franziska Zickmann and
Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248i256 of BIO, 2011. Keywords: from network, heuristic, integer linear programming, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization. Note: http://dx.doi.org/10.1093/bioinformatics/btr210.
Toggle abstract
"Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multigene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NNtanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. © The Author(s) 2011. Published by Oxford University Press."



JeanPhilippe Doyon,
Vincent Ranwez,
Vincent Daubin and
Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392400, 2011. Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
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"Gene sequences contain a goldmine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Among them, gene duplications, transfers and losses are especially important to identify. These events are crucial to account for when reconstructing the history of species, and they play a fundamental role in the evolution of genomes, the diversification of organisms and the emergence of new cellular functions.We review reconciliations between gene and species trees, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family. Existing reconciliation models and algorithms are reviewed and difficulties in modeling gene transfers are discussed. We also compare different reconciliation programs along with their advantages and disadvantages. © The Author 2011. Published by Oxford University Press."



Changiz Eslahchi and
Reza Hassanzadeh. New Algorithm for Constructing Supernetworks from Partial Trees. In MCCMB11, Pages 106107, 2011. Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network. Note: http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106.



Louxin Zhang,
Yen Kaow Ng,
Taoyang Wu and
Yu Zheng. Network model and efficient method for detecting relative duplications or horizontal gene transfers. In ICCABS11, Pages 214219, 2011. Keywords: dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Toggle abstract
"Background: Horizontal gene transfer and gene duplication are two significant forces behind genome evolution. As more and more wellsupported examples of HGTs are being revealed, there is a growing awareness that HGT is more widespread than previously thought, occurring often not only within bacteria, but also between species remotely related such as bacteria and plants or plants and animals. Although a substantial number of genomic sequences are known, HGT inference remains challenging. Parsimonybased inferences of HGT events are typically NPhard under the framework of gene tree and species tree comparison; it is even more timeconsuming if the maximum likelihood approach is used. The fact that gene tree and species tree incongruence can be further confounded by gene duplication and gene loss events motivates us to incorporate considerations for these events into our inference of HGT events. Similarly, it will be beneficial if known HGT events are considered in the inference of gene duplications and gene losses. © 2011 IEEE."



Jaroslaw Byrka,
Pawel Gawrychowski,
Katharina Huber and
Steven Kelk. Worstcase optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):6575, 2010. Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/0710.3258.
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"The study of phylogenetic networks is of great interest to computational evolutionary biology and numerous different types of such structures are known. This article addresses the following question concerning rooted versions of phylogenetic networks. What is the maximum value of p ∈ [0, 1] such that for every input set T of rooted triplets, there exists some network N such that at least p  T  of the triplets are consistent with N? We call an algorithm that computes such a network (where p is maximum) worstcase optimal. Here we prove that the set containing all triplets (the full triplet set) in some sense defines p. Moreover, given a network N that obtains a fraction p′ for the full triplet set (for any p′), we show how to efficiently modify N to obtain a fraction ≥ p′ for any given triplet set T. We demonstrate the power of this insight by presenting a worstcase optimal result for level1 phylogenetic networks improving considerably upon the 5/12 fraction obtained recently by Jansson, Nguyen and Sung. For level2 phylogenetic networks we show that p ≥ 0.61. We emphasize that, because we are taking  T  as a (trivial) upper bound on the size of an optimal solution for each specific input T, the results in this article do not exclude the existence of approximation algorithms that achieve approximation ratio better than p. Finally, we note that all the results in this article also apply to weighted triplet sets. © 2009 Elsevier B.V. All rights reserved."



ZhiZhong Chen and
Lusheng Wang. HybridNET: a tool for constructing hybridization networks. In BIO, Vol. 26(22):29122913, 2010. Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNET, software. Note: http://rnc.r.dendai.ac.jp/~chen/papers/note2.pdf.
Toggle abstract
"Motivations: When reticulation events occur, the evolutionary history of a set of existing species can be represented by a hybridization network instead of an evolutionary tree. When studying the evolutionary history of a set of existing species, one can obtain a phylogenetic tree of the set of species with high confidence by looking at a segment of sequences or a set of genes. When looking at another segment of sequences, a different phylogenetic tree can be obtained with high confidence too. This indicates that reticulation events may occur. Thus, we have the following problem: given two rooted phylogenetic trees on a set of species that correctly represent the treelike evolution of different parts of their genomes, what is the hybridization network with the smallest number of reticulation events to explain the evolution of the set of species under consideration? Results: We develop a program, named HybridNet, for constructing a hybridization network with the minimum number of reticulate vertices from two input trees. We first implement the O(3dn)time algorithm by Whidden et al. for computing a maximum (acyclic) agreement forest. Our program can output all the maximum (acyclic) agreement forests. We then augment the program so that it can construct an optimal hybridization network for each given maximum acyclic agreement forest. To our knowledge, this is the first time that optimal hybridization networks can be rapidly constructed. © The Author 2010. Published by Oxford University Press. All rights reserved."



Leo van Iersel,
Steven Kelk,
Regula Rupp and
Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124i131 of BIO, 2010. Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.
Toggle abstract
"Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a dataset cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events, such as hybridizations, recombinations and horizontal gene transfers. Here, we present the new CASS algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by CASS are usually simpler than networks constructed by other available methods. Moreover, we show that CASS is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented CASS and integrated it into the freely available Dendroscope software. Contact: l.j.j.v.iersel@gmail.com. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press."



Tetsuo Asano,
Jesper Jansson,
Kunihiko Sadakane,
Ryuhei Uehara and
Gabriel Valiente. Faster Computation of the RobinsonFoulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190201 of LNCS, springer, 2010. Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread. Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.
Toggle abstract
"The RobinsonFoulds distance, which is the most widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two networks N1,N2 with n leaves, m nodes, and e edges, the RobinsonFoulds distance measures the number of clusters of descendant leaves that are not shared by N1 and N2. The fastest known algorithm for computing the RobinsonFoulds distance between those networks runs in O(m(m + e)) time. In this paper, we improve the time complexity to O(n(m+ e)/ log n) for general networks and O(nm/log n) for general networks with bounded degree, and to optimal O(m + e) time for planar phylogenetic networks and boundedlevel phylogenetic networks.We also introduce the natural concept of the minimum spread of a phylogenetic network and show how the running time of our new algorithm depends on this parameter. As an example, we prove that the minimum spread of a levelk phylogenetic network is at most k + 1, which implies that for two levelk phylogenetic networks, our algorithm runs in O((k + 1)(m + e)) time. © SpringerVerlag Berlin Heidelberg 2010."



Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140i148 of BIO, 2010. Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software. Note: http://dx.doi.org/10.1093/bioinformatics/btq198.
Toggle abstract
"Motivation: Reticulate network is a model for displaying and quantifying the effects of complex reticulate processes on the evolutionary history of species undergoing reticulate evolution. A central computational problem on reticulate networks is: given a set of phylogenetic trees (each for some region of the genomes), reconstruct the most parsimonious reticulate network (called the minimum reticulate network) that combines the topological information contained in the given trees. This problem is wellknown to be NPhard. Thus, existing approaches for this problem either work with only two input trees or make simplifying topological assumptions. Results: We present novel results on the minimum reticulate network problem. Unlike existing approaches, we address the fully general problem: there is no restriction on the number of trees that are input, and there is no restriction on the form of the allowed reticulate network. We present lower and upper bounds on the minimum number of reticulation events in the minimum reticulate network (and infer an approximately parsimonious reticulate network). A program called PIRN implements these methods, which also outputs a graphical representation of the inferred network. Empirical results on simulated and biological data show that our methods are practical for a wide range of data. More importantly, the lower and upper bounds match for many datasets (especially when the number of trees is small or reticulation level is low), and this allows us to solve the minimum reticulate network problem exactly for these datasets. Availability: A software tool, PIRN, is available for download from the web page: http://www.engr.uconn.edu/ywu. Contact: ywu@engr.uconn.edu. Supplementary information: Supplementary data is available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press."



Yufeng Wu and
Jiayin Wang. Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In ISBRA10, Vol. 6053:203214 of LNCS, springer, 2010. Keywords: agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance. Note: http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf.
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"Hybridization is a reticulate evolutionary process. An established problem on hybridization is computing the minimum number of hybridization events, called the hybridization number, needed in the evolutionary history of two phylogenetic trees. This problem is known to be NPhard. In this paper, we present a new practical method to compute the exact hybridization number. Our approach is based on an integer linear programming formulation. Simulation results on biological and simulated datasets show that our method (as implemented in program SPRDist) is more efficient and robust than an existing method. © 2010 SpringerVerlag Berlin Heidelberg."





Gabriel Cardona,
Francesc Rosselló and
Gabriel Valiente. Comparison of treechild phylogenetic networks. In TCBB, Vol. 6(4):552569, 2009. Keywords: explicit network, phylogenetic network, phylogeny, Program Bio PhyloNetwork, Program PhyloNetwork, tree child network, tree sibling network. Note: http://arxiv.org/abs/0708.3499.
Toggle abstract
"Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a wellfounded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called treechild phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the wellknown RobinsonFoulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a treechild phylogenetic network from its path multiplicity vectors, for computing the distance between two treechild phylogenetic networks and for aligning a pair of treechild phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/ phylonetworks/mudistance/. © 2009 IEEE."



Leo van Iersel,
Steven Kelk and
Matthias Mnich. Uniqueness, intractability and exact algorithms: reflections on levelk phylogenetic networks. In JBCB, Vol. 7(4):597623, 2009. Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://arxiv.org/pdf/0712.2932v2.



Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009. Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction. Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.



ThuHien To and
Michel Habib. Levelk Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time. In CPM09, (5577):275288, springer, 2009. Keywords: explicit network, from triplets, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/0901.1657.
Toggle abstract
"For a given dense triplet set Τ there exist two natural questions [7]: Does there exist any phylogenetic network consistent with Τ? In case such networks exist, can we find an effective algorithm to construct one? For cases of networks of levels k = 0, 1 or 2, these questions were answered in [1,6,7,8,10] with effective polynomial algorithms. For higher levels k, partial answers were recently obtained in [11] with an O(/Τ/k+1)time algorithm for simple networks. In this paper, we give a complete answer to the general case, solving a problem proposed in [7]. The main idea of our proof is to use a special property of SNsets in a levelk network. As a consequence, for any fixed k, we can also find a levelk network with the minimum number of reticulations, if one exists, in polynomial time. © 2009 Springer Berlin Heidelberg."



Philippe Gambette,
Vincent Berry and
Christophe Paul. The structure of levelk phylogenetic networks. In CPM09, Vol. 5577:289300 of LNCS, springer, 2009. Keywords: coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon. Note: http://hallirmm.ccsd.cnrs.fr/lirmm00371485/en/.
Toggle abstract
"Evolution is usually described as a phylogenetic tree, but due to some exchange of genetic material, it can be represented as a phylogenetic network which has an underlying tree structure. The notion of level was recently introduced as a parameter on realistic kinds of phylogenetic networks to express their complexity and treelikeness. We study the structure of levelk networks, and how they can be decomposed into levelk generators. We also provide a polynomial time algorithm which takes as input the set of levelk generators and builds the set of level(k + 1) generators. Finally, with a simulation study, we evaluate the proportion of levelk phylogenetic networks among networks generated according to the coalescent model with recombination. © 2009 Springer Berlin Heidelberg."



Daniel H. Huson,
Regula Rupp,
Vincent Berry,
Philippe Gambette and
Christophe Paul. Computing Galled Networks from Real Data. In ISMBECCB09, Vol. 25(12):i85i93 of BIO, 2009. Keywords: abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction. Note: http://hallirmm.ccsd.cnrs.fr/lirmm00368545/en/.
Toggle abstract
"Motivation: Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although promising approaches exist, there are no tools available that biologists could easily and routinely use to compute rooted phylogenetic networks on real datasets containing tens or hundreds of taxa. Biologists are interested in clades, i.e. groups of monophyletic taxa, and these are usually represented by clusters in a rooted phylogenetic tree. The problem of computing an optimal rooted phylogenetic network from a set of clusters, is hard, in general. Indeed, even the problem of just determining whether a given network contains a given cluster is hard. Hence, some researchers have focused on topologically restricted classes of networks, such as galled trees and levelk networks, that are more tractable, but have the practical drawback that a given set of clusters will usually not possess such a representation. Results: In this article, we argue that galled networks (a generalization of galled trees) provide a good tradeoff between level of generality and tractability. Any set of clusters can be represented by some galled network and the question whether a cluster is contained in such a network is easy to solve. Although the computation of an optimal galled network involves successively solving instances of two different NPcomplete problems, in practice our algorithm solves this problem exactly on large datasets containing hundreds of taxa and many reticulations in seconds, as illustrated by a dataset containing 279 prokaryotes. © 2009 The Author(s)."



Laxmi Parida,
Asif Javed,
Marta Melé,
Francesc Calafell,
Jaume Bertranpetit and
Genographic Consortium. Minimizing recombinations in consensus networks for phylogeographic studies. In BMCB, Vol. 10(Suppl 1):S72, 2009. Note: Selected papers from the Seventh AsiaPacific Bioinformatics Conference (APBC 2009), http://dx.doi.org/10.1186/1471210510S1S72.
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"Background: We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation and recombination events, defined on overlapping sets of extant units the objective is to compute a consensus network G3 with minimum number of additional recombinations. We describe a polynomial time algorithm with a guarantee that the number of computed new recombination events is within = sz(G1, G2) (function sz is a wellbehaved function of the sizes and topologies of G1 and G2) of the optimal number of recombinations. To date, this is the best known result for a network consensus problem. Results: Although the network consensus problem can be applied to a variety of domains, here we focus on structure of human populations. With our preliminary analysis on a segment of the human Chromosome X data we are able to infer ancient recombinations, populationspecific recombinations and more, which also support the widely accepted 'Out of Africa' model. These results have been verified independently using traditional manual procedures. To the best of our knowledge, this is the first recombinationsbased characterization of human populations. Conclusion: We show that our mathematical model identifies recombination spots in the individual haplotypes; the aggregate of these spots over a set of haplotypes defines a recombinational landscape that has enough signal to detect continental as well as population divide based on a short segment of Chromosome X. In particular, we are able to infer ancient recombinations, populationspecific recombinations and more, which also support the widely accepted 'Out of Africa' model. The agreement with mutationbased analysis can be viewed as an indirect validation of our results and the model. Since the model in principle gives us more information embedded in the networks, in our future work, we plan to investigate more nontraditional questions via these structures computed by our methodology. © 2009 Parida et al; licensee BioMed Central Ltd."



Josh Voorkamp né Collins. Rekernelisation Algorithms in Hybrid Phylogenies. Master's thesis, University of Canterbury, New Zealand, 2009. Keywords: agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software. Note: http://hdl.handle.net/10092/2852.



Gabriel Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R. Pages 184208, Taylor & Francis/CRC Press, 2009. Keywords: counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree child network, tree sibling network. Note: http://books.google.fr/books?id=F4YIIUWb7yMC.





Chris Whidden and
Norbert Zeh. A Unifying View on Approximation and FPT of Agreement Forests. In WABI09, Vol. 5724:390402 of LNCS, Springer, 2009. Keywords: agreement forest, approximation, explicit network, FPT, minimum number, phylogenetic network, phylogeny, reconstruction. Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS200902.pdf.
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"We provide a unifying view on the structure of maximum (acyclic) agreement forests of rooted and unrooted phylogenies. This enables us to obtain linear or O(n log n)time 3approximation and improved fixedparameter algorithms for the subtree prune and regraft distance between two rooted phylogenies, the tree bisection and reconnection distance between two unrooted phylogenies, and the hybridization number of two rooted phylogenies. © 2009 Springer Berlin Heidelberg."



Gabriel Cardona,
Francesc Rosselló and
Gabriel Valiente. Tripartitions do not always discriminate phylogenetic networks. In MBIO, Vol. 211(2):356370, 2008. Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree child network, tripartition distance. Note: http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/.
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"Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the socalled tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric. © 2007 Elsevier Inc. All rights reserved."



Leo van Iersel,
Judith Keijsper,
Steven Kelk,
Leen Stougie,
Ferry Hagen and
Teun Boekhout. Constructing level2 phylogenetic networks from triplets. In RECOMB08, Vol. 4955:450462 of LNCS, springer, 2008. Keywords: explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction. Note: http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890.
Toggle abstract
"Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontreelike. This further strengthens the case for the use of tripletbased methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data. © 2009 IEEE."





Gabriel Cardona,
Francesc Rosselló and
Gabriel Valiente. A Perl Package and an Alignment Tool for Phylogenetic Networks. In BMCB, Vol. 9:175, 2008. Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree child network, tree sibling network. Note: http://dx.doi.org/10.1186/147121059175.
Toggle abstract
"Background: Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none of which are opensource libraries, and they do not allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning them. Results: In order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by him or herself. Conclusion: The Perl package is available as part of the BioPerl bundle, and can also be downloaded. A webbased application is also available (see availability and requirements). The Perl package includes full documentation of all its features. © 2008 Cardona et al; licensee BioMed Central Ltd."



Rune Lyngsø,
Yun S. Song and
Jotun Hein. Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony. In RECOMB08, Vol. 4955:463477 of LNCS, springer, 2008. Keywords: coalescent, likelihood, phylogenetic network, phylogeny, recombination, statistical model. Note: http://dx.doi.org/10.1007/9783540788393_41.
Toggle abstract
"Understanding the variation of recombination rates across a given genome is crucial for disease gene mapping and for detecting signatures of selection, to name just a couple of applications. A widelyused method of estimating recombination rates is the maximum likelihood approach, and the problem of accurately computing likelihoods in the coalescent with recombination has received much attention in the past. A variety of sampling and approximation methods have been proposed, but no single method seems to perform consistently better than the rest, and there still is great value in developing better statistical methods for accurately computing likelihoods. So far, with the exception of some twolocus models, it has remained unknown how the true likelihood exactly behaves as a function of model parameters, or how close estimated likelihoods are to the true likelihood. In this paper, we develop a deterministic, parsimonybased method of accurately computing the likelihood for multilocus input data of moderate size. We first find the set of all ancestral configurations (ACs) that occur in evolutionary histories with at most k crossover recombinations. Then, we compute the likelihood by summing over all evolutionary histories that can be constructed only using the ACs in that set. We allow for an arbitrary number of crossing over, coalescent and mutation events in a history, as long as the transitions stay within that restricted set of ACs. For given parameter values, by gradually increasing the bound k until the likelihood stabilizes, we can obtain an accurate estimate of the likelihood. At least for moderate crossover rates, the algorithmbased method described here opens up a new window of opportunities for testing and finetuning statistical methods for computing likelihoods. © 2008 SpringerVerlag Berlin Heidelberg."





Leo van Iersel and
Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ISAAC08, Vol. 5369:472483 of LNCS, springer, 2008. Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic. Note: http://arxiv.org/abs/0805.1859.



Cuong Than and
Luay Nakhleh. SPRbased Tree Reconciliation: Nonbinary Trees and Multiple Solutions. In APBC08, Pages 251260, 2008. Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance. Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.



Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, EberhardKarlsUniversität Tübingen, Germany, 2008. Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization. Note: https://publikationen.unituebingen.de/xmlui/handle/10900/49159.



Daniel H. Huson and
Regula Rupp. Summarizing Multiple Gene Trees Using Cluster Networks. In WABI08, Vol. 5251:296305 of LNCS, springer, 2008. Keywords: abstract network, from clusters, from rooted trees, phylogenetic network, phylogeny, polynomial, Program Dendroscope. Note: http://dx.doi.org/10.1007/9783540873617_25, slides from the MIEP Conference available at http://www.lirmm.fr/MIEP08/slides/11_13_rupp.pdf.
Toggle abstract
"The result of a multiple gene tree analysis is usually a number of different tree topologies that are each supported by a significant proportion of the genes. We introduce the concept of a cluster network that can be used to combine such trees into a single rooted network, which can be drawn either as a cladogram or phylogram. In contrast to split networks, which can grow exponentially in the size of the input, cluster networks grow only quadratically. A cluster network is easily computed using a modification of the treepopping algorithm, which we call networkpopping. The approach has been implemented as part of the Dendroscope treedrawing program and its application is illustrated using data and results from three recent studies on large numbers of gene trees. © 2008 SpringerVerlag Berlin Heidelberg."



Lichen Bao and
Sergey Bereg. Clustered SplitsNetworks. In COCOA08, Vol. 5165:469478 of LNCS, springer, 2008. Keywords: abstract network, from distances, NeighborNet, realization, reconstruction. Note: http://dx.doi.org/10.1007/9783540850977_44, slides available at http://www.utdallas.edu/~besp/cocoa08talk.pdf.
Toggle abstract
"We address the problem of constructing phylogenetic networks using two criteria: the number of cycles and the fit value of the network. Traditionally the fit value is the main objective for evaluating phylogenetic networks. However, a small number of cycles in a network is desired and pointed out in several publications. We propose a new phylogenetic network called CSnetwork and a method for constructing it. The method is based on the wellknown splitstree method. A CSnetwork contains a face which is kcycle, k ≥ 3 (not as splitstree). We discuss difficulties of using nonparallelogram faces in splitstree networks. Our method involves clustering and optimization of weights of the network edges. The algorithm for constructing the underlying graph (except the optimization step) has a polynomial time. Experimental results show a good performance of our algorithm. © SpringerVerlag Berlin Heidelberg 2008."



Sagi Snir and
Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In WABI08, Vol. 5251:354368 of LNCS, springer, 2008. Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model. Note: http://dx.doi.org/10.1007/9783540873617_30.
Toggle abstract
"Horizontal Gene Transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model for analyzing and modeling phylogenetic networks, the NETHMM. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NETHMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NETHMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NETHMM) to a given data set. Using NETHMM we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and two different biological inputs. © 2008 SpringerVerlag Berlin Heidelberg."



Stefan Grünewald,
Andreas Spillner,
Kristoffer Forslund and
Vincent Moulton. Constructing Phylogenetic Supernetworks from Quartets. In WABI08, Vol. 5251:284295 of LNCS, springer, 2008. Keywords: abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network. Note: http://dx.doi.org/10.1007/9783540873617_24.
Toggle abstract
"In phylogenetics it is common practice to summarize collections of partial phylogenetic trees in the form of supertrees. Recently it has been proposed to construct phylogenetic supernetworks as an alternative to supertrees as these allow the representation of conflicting information in the trees, information that may not be representable in a single tree. Here we introduce SuperQ, a new method for constructing such supernetworks. It works by breaking the input trees into quartet trees, and stitching together the resulting set to form a network. The stitching process is performed using an adaptation of the QNet method for phylogenetic network reconstruction. In addition to presenting the new method, we illustrate the applicability of SuperQ to three data sets and discuss future directions for testing and development. © 2008 SpringerVerlag Berlin Heidelberg."





Gabriel Cardona,
Francesc Rosselló and
Gabriel Valiente. Extended Newick: It is Time for a Standard Representation. In BMCB, Vol. 9:532, 2008. Keywords: evaluation, explicit network, phylogenetic network, Program Bio PhyloNetwork, Program Dendroscope, Program NetGen, Program PhyloNet, Program SplitsTree, Program TCS, visualization. Note: http://bioinfo.uib.es/media/uploaded/bmc2008enewicksub.pdf.





Daniel H. Huson and
Tobias Kloepper. Beyond Galled Trees  Decomposition and Computation of Galled Networks. In RECOMB07, Vol. 4453:211225 of LNCS, springer, 2007. Keywords: FPT, from splits, from trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction. Note: http://dx.doi.org/10.1007/9783540716815_15, errata..





Guohua Jin,
Luay Nakhleh,
Sagi Snir and
Tamir Tuller. A New Lineartime Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In ISBRA07, Vol. 4463:6172 of LNCS, springer, 2007. Keywords: approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal. Note: http://www.cs.rice.edu/~nakhleh/Papers/isbra07.pdf.





Cam Thach Nguyen,
Nguyen Bao Nguyen and
WingKin Sung. Fast Algorithms for computing the Tripartitionbased Distance between Phylogenetic Networks. In JCO, Vol. 13(3), 2007. Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance. Note: http://dx.doi.org/10.1007/s1087800690255.
Toggle abstract
"Consider two phylogenetic networks N and N′ of size n. The tripartitionbased distance finds the proportion of tripartitions which are not shared by N and N′. This distance is proposed by Moret et al. (2004) and is a generalization of RobinsonFoulds distance, which is orginally used to compare two phylogenetic trees. This paper gives an O(min {kn log n, n log n + hn} time algorithm to compute this distance, where h is the number of hybrid nodes in N and N′ while k is the maximum number of hybrid nodes among all biconnected components in N and N′. Note that k ≪ h ≪ n in a phylogenetic network. In addition, we propose algorithms for comparing galledtrees, which are an important, biological meaningful special case of phylogenetic network. We give an O(n)time algorithm for comparing two galledtrees. We also give an O(n + kh)time algorithm for comparing a galledtree with another general network, where h and k are the number of hybrid nodes in the latter network and its biggest biconnected component respectively. © Springer Science+Business Media, LLC 2007."





Maria S. Poptsova and
J. Peter Gogarten. The power of phylogenetic approaches to detect horizontally transferred genes. In BMCEB, Vol. 7(45), 2007. Keywords: evaluation, from rooted trees, lateral gene transfer, Program EEEP. Note: http://dx.doi.org/10.1186/14712148745.
Toggle abstract
"Background. Horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. High genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. Does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? The answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred genes from further analyses. Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods? Results. Phylogenetic detection methods appear to be the method of choice to infer gene transfers, especially for ancient transfers and those followed by orthologous replacement. Here we explore how well some of these methods perform using in silico transfers between the terminal branches of a gamma proteobacterial, genome based phylogeny. For the experiments performed here on average the AU test at a 5% significance level detects 90.3% of the transfers and 91% of the exchanges as significant. Using the RobinsonFoulds distance only 57.7% of the exchanges and 60% of the donations were identified as significant. Analyses using bipartition spectra appeared most successful in our test case. The power of detection was on average 97% using a 70% cutoff and 94.2% with 90% cutoff for identifying conflicting bipartitions, while the rate of false positives was below 4.2% and 2.1% for the two cutoffs, respectively. For all methods the detection rates improved when more intervening branches separated donor and recipient. Conclusion. Rates of detected transfers should not be mistaken for the actual transfer rates; most analyses of gene transfers remain anecdotal. The method and significance level to identify potential gene transfer events represent a tradeoff between the frequency of erroneous identification (false positives) and the power to detect actual transfer events. © 2007 Poptsova and Gogarten; licensee BioMed Central Ltd."





Yun S. Song,
Zhihong Ding,
Dan Gusfield,
Charles Langley and
Yufeng Wu. Algorithms to Distinguish the Role of GeneConversion from SingleCrossover Recombination in the Derivation of SNP Sequences in Populations. In JCB, Vol. 14(10):12731286, 2007. Keywords: ARG, from sequences, phylogenetic network, phylogeny, Program SHRUB, reconstruction. Note: http://dx.doi.org/10.1089/cmb.2007.0096.
Toggle abstract
"Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is "association mapping" in populations, which is widely hoped to help find genes that influence genetic diseases (Carlson et al., 2004; Clark, 2003). Hence, a great deal of recent attention has focused on problems of inferring the historical derivation of sequences in populations when both mutations and recombinations have occurred. In the algorithms literature, most of that recent work has been directed to singlecrossover recombination. However, geneconversion is an important, and more common, form of (twocrossover) recombination which has been much less investigated in the algorithms literature. In this paper, we explicitly incorporate geneconversion into discrete methods to study historical recombination. We are concerned with algorithms for identifying and locating the extent of historical crossingover and geneconversion (along with singlenucleotide mutation), and problems of constructing full putative histories of those events. The novel technical issues concern the incorporation of geneconversion into recently developed discrete methods (Myers and Griffiths, 2003; Song et al., 2005) that compute lower and upperbound information on the amount of needed recombination without geneconversion. We first examine the most natural extension of the lower bound methods from Myers and Griffiths (2003), showing that the extension can be computed efficiently, but that this extension can only yield weak lower bounds. We then develop additional ideas that lead to higher lower bounds, and show how to solve, via integerlinear programming, a more biologically realistic version of the lower bound problem. We also show how to compute effective upper bounds on the number of needed singlecrossovers and geneconversions, along with explicit networks showing a putative history of mutations, singlecrossovers and geneconversions. Both lower and upper bound methods can handle data with missing entries, and the upper bound method can be used to infer missing entries with high accuracy. We validate the significance of these methods by showing that they can be effectively used to distinguish simulationderived sequences generated without geneconversion from sequences that were generated with geneconversion. We apply the methods to recently studied sequences of Arabidopsis thaliana, identifying many more regions in the sequences than were previously identified (Plagnol et al., 2006), where geneconversion may have played a significant role. Demonstration software is available at www.csif.cs.ucdavis.edu/∼gusfield. © 2007 Mary Ann Liebert, Inc."





Yuanyi Zhang. Optimization Algorithms for Phylogenetic Networks. PhD thesis, University of Texas at Dallas, U.S.A., 2007. Keywords: abstract network, explicit network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network, visualization. Note: http://proquest.umi.com/pqdlink?did=1421626541&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.



Hadas Birin,
Zohar GalOr,
Isaac Elias and
Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111123 of LNCS, springer, 2007. Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction. Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.





Jesper Jansson,
Nguyen Bao Nguyen and
WingKin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SICOMP, Vol. 35(5):10981121, 2006. 1 comment Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf.
Toggle abstract
"This paper considers the problem of determining whether a given set Τ of rooted triplets can be merged without conflicts into a galled phylogenetic network and, if so, constructing such a network. When the input Τ is dense, we solve the problem in O(Τ) time, which is optimal since the size of the input is Θ(Τ). In comparison, the previously fastest algorithm for this problem runs in O(Τ2) time. We also develop an optimal O(Τ)time algorithm for enumerating all simple phylogenetic networks leaflabeled by L that are consistent with Τ, where L is the set of leaf labels in Τ, which is used by our main algorithm. Next, we prove that the problem becomes NPhard if extended to nondense inputs, even for the special case of simple phylogenetic networks. We also show that for every positive integer n, there exists some set Τ of rooted triplets on n leaves such that any galled network can be consistent with at most 0.4883 ·Τ of the rooted triplets in Τ. On the other hand, we provide a polynomialtime approximation algorithm that always outputs a galled network consistent with at least a factor of 5/12 (> 0.4166) of the rooted triplets in Τ. © 2006 Society for Industrial and Applied Mathematics."







Sergey Bereg and
Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In BIBE05, Pages 320323, 2005. Note: http://dx.doi.org/10.1109/BIBE.2005.46.
Toggle abstract
A classical result in phylogenetic trees is that a binary phylogenetic tree adhering to the molecular clock hypothesis exists if and only if the matrix of distances between taxa is ultrametric. The ultrametric condition is very restrictive. In this paper we study phylogenetic networks that can be constructed assuming the molecular clock hypothesis. We characterize distance matrices that admit such networks for 3 and 4 taxa. We design an efficient algorithm for a special class of phylogenetic networks that can detect the existence of a network and constructs it. © 2005 IEEE.





Elena Dubrova. Phylogenetic networks with edgedisjoint recombination cycles. In Proceedings of SPIE Bioengineered and Bioinspired Systems II (SPIEBBS II), Vol. 5839:381388, 2005. Keywords: galled tree, phylogenetic network, polynomial, site consistency. Note: http://dx.doi.org/10.1117/12.607910.
Toggle abstract
"Phylogenetic analysis is a branch of biology that establishes the evolutionary relationships between living organisms. The goal of phylogenetic analysis is to determine the order and approximate timing of speciation events in the evolution of a given set of species. Phylogenetic networks allow to represent evolutionary histories that include events like recombination and hybridization. In this paper, we introduce a class of phylogenetic networks called extended galledtrees in which recombination cycles share no edge. We show that the site consistency problem, which is NPhard in general, can be solved in polynomial time for this class of phylogenetic networks."





Trinh N. D. Huynh,
Jesper Jansson,
Nguyen Bao Nguyen and
WingKin Sung. Constructing a Smallest Refining Galled Phylogenetic Network. In RECOMB05, Vol. 3500:265280 of LNCS, springer, 2005. Keywords: from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction. Note: http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf.



Daniel H. Huson,
Tobias Kloepper,
Peter J. Lockhart and
Mike Steel. Reconstruction of Reticulate Networks from Gene Trees. In RECOMB05, Vol. 3500:233249 of LNCS, springer, 2005. Keywords: from rooted trees, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization. Note: http://dx.doi.org/10.1007/11415770_18.



Daniel H. Huson and
Tobias Kloepper. Computing recombination networks from binary sequences. In ECCB05, Vol. 21(suppl. 2):ii159ii165 of BIO, 2005. Keywords: from sequences, phylogenetic network, phylogeny, recombination. Note: http://dx.doi.org/10.1093/bioinformatics/bti1126.
Toggle abstract
"Motivation:Phylogenetic networks are becoming an important tool in molecular evolution, as the evolutionary role of reticulate events, such as hybridization, horizontal gene transfer and recombination, is becoming more evident, and as the available data is dramatically increasing in quantity and quality. Results: This paper addresses the problem of computing a most parsimonious recombination network for an alignment of binary sequences that are assumed to have arisen under the 'infinite sites' model of evolution with recombinations. Using the concept of a splits network as the underlying datastructure, this paper shows how a recent method designed for the computation of hybridization networks can be extended to also compute recombination networks. A robust implementation of the approach is provided and is illustrated using a number of real biological datasets. © The Author 2005. Published by Oxford University Press. All rights reserved."





Rune Lyngsø,
Yun S. Song and
Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239250 of LNCS, springer, 2005. Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software. Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05239.pdf.



Luay Nakhleh and
LiSan Wang. Phylogenetic Networks, Trees, and Clusters. In IWBRA05, Vol. 3515:919926 of LNCS, springer, 2005. Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment. Note: http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf.



Luay Nakhleh and
LiSan Wang. Phylogenetic Networks: Properties and Relationship to Trees and Clusters. In TCSB2, Vol. 3680:8299 of LNCS, springer, 2005. Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment. Note: http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf.







Yun S. Song,
Yufeng Wu and
Dan Gusfield. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. In ISMB05, Vol. 21:i413i422 of BIO, 2005. Keywords: integer linear programming, minimum number, Program HapBound, Program SHRUB, recombination. Note: http://dx.doi.org/10.1093/bioinformatics/bti1033.
Toggle abstract
"Motivation: We are interested in studying the evolution of DNA single nucleotide polymorphism sequences which have undergone (meiotic) recombination. For a given set of sequences, computing the minimum number of recombinations needed to explain the sequences (with one mutation per site) is a standard question of interest, but it has been shown to be NPhard, and previous algorithms that compute it exactly work either only on very small datasets or on problems with special structure. Results: In this paper, we present efficient, practical methods for computing both upper and lower bounds on the minimum number of needed recombinations, and for constructing evolutionary histories that explain the input sequences. We study in detail the efficiency and accuracy of these algorithms on both simulated and real data sets. The algorithms produce very close upper and lower bounds, which match exactly in a surprisingly wide range of data. Thus, with the use of new, very effective lower bounding methods and an efficient algorithm for computing upper bounds, this approach allows the efficient, exact computation of the minimum number of needed recombinations, with high frequency in a large range of data. When upper and lower bounds match, evolutionary histories found by our algorithm correspond to the most parsimonious histories. © The Author 2005. Published by Oxford University Press. All rights reserved."



Bhaskar DasGupta,
Sergio Ferrarini,
Uthra Gopalakrishnan and
Nisha Raj Paryani. Inapproximability results for the lateral gene transfer problem. In Proceedings of the Ninth Italian Conference on Theoretical Computer Science (ICTCS'05), Pages 182195, springer, 2005. Keywords: approximation, from rooted trees, from species tree, inapproximability, lateral gene transfer, parsimony, phylogenetic network, phylogeny. Note: http://www.cs.uic.edu/~dasgupta/resume/publ/papers/ictcsfinal.pdf.



Insa Cassens,
Patrick Mardulyn and
Michel C. Milinkovitch. Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach? In Systematic Biology, Vol. 54(3):363372, 2005. Keywords: abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software. Note: http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf.



Charles Choy,
Jesper Jansson,
Kunihiko Sadakane and
WingKin Sung. Computing the maximum agreement of phylogenetic networks. In Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS'04), Vol. 91:134147 of Electronic Notes in Theoretical Computer Science, 2004. Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny. Note: http://www.df.lth.se/~jj/Publications/masn6_CATS2004.pdf.
Toggle abstract
"We introduce the maximum agreement phylogenetic subnetwork problem (MASN) of finding a branching structure shared by a set of phylogenetic networks. We prove that the problem is NPhard even if restricted to three phylogenetic networks and give an O(n2)time algorithm for the special case of two level1 phylogenetic networks, where n is the number of leaves in the input networks and where N is called a levelf phylogenetic network if every biconnected component in the underlying undirected graph contains at most f nodes having indegree 2 in N. Our algorithm can be extended to yield a polynomialtime algorithm for two levelf phylogenetic networks N 1,N2 for any f which is upperbounded by a constant; more precisely, its running time is O(V(N1)·V(N 2)·4f), where V(Ni) denotes the set of nodes of Ni. © 2004 Published by Elsevier B.V."



Jesper Jansson and
WingKin Sung. Inferring a level1 phylogenetic network from a dense set of rooted triplets. In COCOON04, Vol. 3106:462471 of LNCS, springer, 2004. 1 comment Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.df.lth.se/~jj/Publications/ipnrt6_COCOON2004.pdf.



Luay Nakhleh,
Tandy Warnow and
C. Randal Linder. Reconstructing reticulate evolution in species  theory and practice. In RECOMB04, Pages 337346, 2004. Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software. Note: http://www.cs.rice.edu/~nakhleh/Papers/144nakhleh.pdf.



Mike Hallett,
Jens Lagergren and
Ali Tofigh. Simultaneous Identification of Duplications and Lateral Transfers. In RECOMB04, Pages 347356, 2004. Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.nada.kth.se/~jensl/p164hallett.pdf.









Pawel Górecki. Reconciliation problems for duplication, loss and horizontal gene transfer. In RECOMB04, Pages 316325, 2004. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://ai.stanford.edu/~serafim/CS374_2004/Papers/Gorecki_Reconciliation.pdf.







Luay Nakhleh,
Jerry Sun,
Tandy Warnow,
C. Randal Linder,
Bernard M. E. Moret and
Anna Tholse. Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. In PSB03, 2003. Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance. Note: http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf.







Pawel Górecki. Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model. In ECCB03, 2003. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.inra.fr/eccb2003/posters/pdf/short/S_gorecki.ps.



David Bryant and
Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375391 of LNCS, springer, 2002. Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network. Note: http://dx.doi.org/10.1007/3540457844_28.





Lusheng Wang,
Kaizhong Zhang and
Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 4650, 2001. Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction. Note: http://dx.doi.org/10.1145/372202.372271.







Vincent Berry and
David Bryant. Faster reliable phylogenetic analysis. In RECOMB99, Pages 5968, 1999. Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible. Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151.



Bin Ma,
Lusheng Wang and
Ming Li. Fixed topology alignment with recombination. In CPM98, Vol. 1448:174188 of LNCS, springer, 1998. Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination. Note: http://dx.doi.org/10.1007/BFb0030789.





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